Contacts of the helix formed by residues 171 - 181 (chain P) in PDB entry 2I2R
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with PRO 171 (chain P).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148P MET* 4.5 4.2 - - - +
151P VAL* 4.5 12.2 - - + +
152P LYS* 5.4 8.1 - - + +
155P TYR* 4.0 29.2 - - + -
169P ASP 4.2 1.1 - - - +
170P THR* 1.3 85.6 - - - +
172P ARG* 1.3 71.7 + - + +
173P GLN 3.3 1.1 - - - -
174P HIS* 3.1 19.8 + - + +
175P VAL* 3.4 11.6 + - - +
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Residues in contact with ARG 172 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148P MET* 3.8 30.7 - - + +
170P THR* 5.4 1.1 - - - -
171P PRO* 1.3 75.7 - - + +
173P GLN* 1.3 54.1 + - - +
174P HIS 2.7 15.4 + - - -
175P VAL* 3.3 4.0 + - - +
176P ASP* 3.1 30.5 + - - +
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Residues in contact with GLN 173 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168P GLU* 6.0 2.1 - - - +
170P THR* 3.5 27.5 - - - +
171P PRO 3.3 0.6 - - - -
172P ARG* 1.3 74.9 - - - +
174P HIS* 1.3 58.5 + - - +
176P ASP* 4.3 13.9 - - - -
177P VAL* 3.4 21.1 - - - +
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Residues in contact with HIS 174 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19L TRP* 3.7 31.3 - + + +
20L MET 3.7 5.1 + - - -
21L PRO* 3.1 44.8 - - + +
151P VAL* 4.5 9.4 - - + -
155P TYR* 3.2 26.4 + - - -
167P ALA* 3.8 6.7 - - - +
168P GLU* 4.0 6.2 + - + +
170P THR 3.2 13.1 + - - +
171P PRO* 3.1 16.2 - - + +
172P ARG 2.7 3.6 + - - -
173P GLN* 1.3 79.4 + - - +
175P VAL* 1.3 58.3 + - - +
176P ASP 3.2 0.7 - - - -
177P VAL* 3.1 30.8 - - + +
178P PHE* 3.3 9.2 + - - +
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Residues in contact with VAL 175 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144P LYS* 4.2 18.4 - - + +
147P MET* 3.6 15.9 - - + +
148P MET* 3.5 46.2 - - + +
151P VAL* 4.2 10.3 - - + +
171P PRO 3.4 3.5 + - - +
172P ARG 3.3 7.1 + - - +
174P HIS* 1.3 76.9 - - - +
176P ASP* 1.3 65.4 + - - +
178P PHE* 3.2 8.7 - - - +
179P PHE* 2.9 52.3 + - + -
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Residues in contact with ASP 176 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144P LYS* 6.1 0.2 - - - +
148P MET* 5.8 2.6 - - - +
172P ARG* 3.1 21.4 + - - +
173P GLN* 4.3 10.1 - - - -
175P VAL* 1.3 84.1 - - - +
177P VAL* 1.3 58.5 + - + +
179P PHE* 4.0 3.9 - - - +
180P GLN* 3.0 33.1 + - - +
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Residues in contact with VAL 177 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18L GLY 5.8 0.2 - - - +
19L TRP* 5.4 4.5 - - + -
173P GLN 3.4 17.3 - - - +
174P HIS* 3.1 30.5 - - + +
176P ASP* 1.3 77.1 - - + +
178P PHE* 1.3 67.4 + - + +
180P GLN* 3.6 3.7 + - - +
181P LYS* 3.2 26.9 + - - +
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Residues in contact with PHE 178 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18L GLY* 2.8 41.1 - - - +
19L TRP* 4.6 8.3 - + + -
134P TYR* 4.4 10.3 - + - -
142P ILE* 4.8 1.3 - - + -
147P MET* 3.5 39.9 - - + -
174P HIS 3.3 9.4 + - - +
175P VAL* 3.2 11.0 - - - +
177P VAL* 1.3 84.6 - - + +
179P PHE* 1.3 69.4 + + - +
181P LYS* 3.3 2.2 - - - -
182P MET* 2.9 61.7 + - + +
190P VAL* 4.5 19.5 - - + -
195P PHE* 4.0 17.3 - + - -
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Residues in contact with PHE 179 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142P ILE* 3.4 21.5 - - + -
143P ASN 3.5 2.5 - - - -
144P LYS* 3.2 40.2 - - + -
147P MET* 4.2 10.1 - - + -
175P VAL* 2.9 38.9 + - + +
176P ASP* 4.1 4.3 - - - +
178P PHE* 1.3 79.4 - + - +
180P GLN* 1.3 62.1 + - - +
181P LYS 3.0 5.2 - - - -
182P MET* 4.4 0.7 - - - -
183P ASP* 2.9 52.9 + - + +
186P LYS* 4.1 1.2 - - - -
188P GLY* 3.4 30.7 - - - -
190P VAL* 4.0 15.0 - - + -
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Residues in contact with GLN 180 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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176P ASP 3.0 19.2 + - - +
177P VAL* 4.3 3.8 - - - +
179P PHE* 1.3 75.3 - - - +
181P LYS* 1.3 57.6 + - - +
182P MET 3.7 0.2 - - - -
183P ASP 5.1 0.8 - - - +
186P LYS* 3.5 32.8 + - - +
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Residues in contact with LYS 181 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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177P VAL 3.2 17.9 + - - +
178P PHE* 3.3 4.7 - - - -
179P PHE 3.0 0.6 - - - -
180P GLN* 1.3 80.7 - - - +
182P MET* 1.3 70.0 + - - +
198P SER* 3.3 5.1 + - - -
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il